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Updated: Oct 14, 2025
10:45
iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
Published on: April 30, 2011
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Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of
Li Cai1, Jiajia Xuan1, Qiao Lin1
1MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Fifth Affiliated Hospital, Sun Yat-sen University, Guangdong, Guangzhou 510275, P.R. China.
Nucleic Acids Research
|November 8, 2021
Summary
Pol3Base is a new resource for studying RNA polymerase III (Pol III)-transcribed non-coding RNAs (ncRNAs). It decodes their interactome, expression, evolution, and disease variations, aiding research into their functions and regulatory networks.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- RNA polymerase III (Pol III) transcribes numerous non-coding RNAs (ncRNAs) crucial for cellular functions.
- The expression, functions, regulatory networks, and evolution of these Pol III-transcribed ncRNAs remain largely unexplored.
Purpose of the Study:
- To develop a comprehensive resource, Pol3Base, for decoding the interactome, expression, evolution, epitranscriptome, and disease variations of Pol III-transcribed ncRNAs.
- To provide a centralized platform for researchers to investigate the roles of these ncRNAs in various biological processes and diseases.
Main Methods:
- Mining ChIP-seq and CLIP-seq datasets to identify regulatory relationships and RNA binding protein interactions.
- Integrating data on RNA modifications, expression profiles across tissues and tumors, evolutionary conservation between human and mouse, and somatic mutation data.
- Developing the Pol3Base database (http://rna.sysu.edu.cn/pol3base/) to host and present these integrated data.
Main Results:
- Pol3Base includes thousands of regulatory relationships for ~79,000 ncRNAs and interactions with >240 RNA binding proteins.
- The resource contains ~9,700 RNA modifications, expression profiles in >70 tissues and 28 tumor types, ~4,000 conserved ncRNAs, and ~11,403 tRNA-derived small RNAs (tsRNAs) in 32 tumor types.
- Analysis of somatic mutation data revealed potential roles of these ncRNAs in diverse diseases.
Conclusions:
- Pol3Base offers a valuable resource for expanding the understanding of Pol III-transcribed ncRNAs.
- The integrated data facilitates research into the functions, regulatory networks, and disease relevance of these ncRNAs.
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